摘要
目的:利用高通量测序技术获得马鞭草Verbena officinalis L.的全长转录组基因信息。方法:通过PacBio Sequel高通量测序平台,对马鞭草根、茎、叶3个部位的混合样品进行全长转录组测序,并基于序列同源性对转录本进行功能注释,得到马鞭草全长转录组的遗传信息。结果:测序数据经过质控后获得197542个高质量的转录本及169063条环形一致性序列(CCS),检测出4955个转录因子。其中161062个(81.53%)转录本在非冗余蛋白(NR)、真核生物相邻类的聚簇(KOG)数据库、京都基因与基因组百科全书(KEGG)、基因本体(GO)数据库、蛋白家族(Pfam)数据库和SwissProt蛋白序列数据库中均得到注释。MISA分析发现54063个简单重复序列(SSR)位点,还预测到70050个长链非编码RNAs(lncRNAs)和45499个信使核糖核酸(mRNAs),并在马鞭草全长转录组中共鉴定到了60个转录本可能参与单萜类化合物的生物合成。结论:利用高通量测序技术和生物信息学分析获得了马鞭草的全长转录组信息特征,可为后期开展马鞭草功能基因鉴定、解析萜类化合物次生代谢途径及其调控机制提供参考。
Objective:To obtain the full-length transcriptome gene information of Verbena officinalis L.using highthroughput sequencing technology.Methods:The mixed samples of roots,stems,and leaves of V.officinalis were subjected to full-length transcriptome sequencing using the PacBio Sequel high-throughput sequencing platform.The transcripts were functionally annotated based on sequence homology,and the genetic information of the full-length transcriptome of V.officinalis was obtained.Results:After quality control,the sequencing data yielded 197542 high-quality transcripts and 169063 circular consensus sequence(CCS)reads.A total of 4955 transcription factors were detected.Among them,161062 transcripts(81.53%)were annotated in the non-redundant protein sequence database(NR),eukaryotic orthologous groups(KOG),kyoto encyclopedia of genes and genomes(KEGG),gene ontology(GO),protein family(Pfam)and SwissProt databases.54063 simple repeat sequences(SSR)loci and 70050 IncRNAs and 45499 mRNAs were predicted.Furthermore,60 transcripts potentially involved in the biosynthesis of terpenoids were identified in the full-length transcriptome of V.officinalis.Conclusion:By utilizing high-throughput sequencing technology and bioinformatics analysis,the full-length transcriptome information of V.officinalis was obtained,providing reference data for future studies on functional gene identification,secondary metabolite pathways,and regulatory mechanisms related to terpenoid compounds in V.officinalis.
作者
黄丽容
欧夏莲
李翠
胡营
韦筱媚
郭晓云
雷明
缪剑华
HUANG Li-rong;OU Xia-lian;LI Cui;HU Ying;WEI Xiao-mei;GUO Xiao-yun;LEI Ming;MIAO Jian-hua(Guangxi Key Laboratory of Medicinal Resources Protection and Genetic Improvement/Guangxi Engineering Research Center of TCM Resource Intelligent Creation,Guangxi Botanical Garden of Medicinal Plants,Nanning 530023,China)
出处
《中国现代中药》
CAS
2023年第7期1486-1495,共10页
Modern Chinese Medicine
基金
广西创新驱动发展专项(桂科AA18242040)
广西自然科学基金面上项目(2020GXNSFAA159151)
对发展中国家科技援助项目(KY201904001)
科技基础资源调查专项(2018FY100700)。
关键词
马鞭草
全长转录组
测序分析
Verbena officinalis L.
full-length transcriptome
sequencing
